Background

This is the skeleton rmd outlining the development of a revised (“new”) QRF model (See et al. 2021). This will eventually highlight the covariate selection process, QRF model fit, the RF extrapolation model, and finally compare extrapolation estimates between the original and new models for eight watersheds within the Upper Salmon Basin.

Covariate selection

Explain covariate selection process. DASH/resto compatible, high MIC, low correlation, missing data, lots of zeros, species specific models, and eventually converting to joint models.

QRF Model fit

Talk about relative importance and pdp plots.

Extrapolation model

Talk about GAA’s

Extrapolation comparison

Extrapolations of habitat capacity for Chinook salmon, by life-stage, within the North Fork Salmon watershed.

Extrapolations of habitat capacity for Chinook salmon, by life-stage, within the North Fork Salmon watershed.

Extrapolations of habitat capacity for steelhead, by life-stage, within the North Fork Salmon watershed..

Extrapolations of habitat capacity for steelhead, by life-stage, within the North Fork Salmon watershed..

QRF Habitat Capacity Estimates

Comparison with previous extrapolation

Chinook Salmon

Change in predicted habitat capacity for Chinook salmon compared to the previous extrapolation, by life-stage, within the North Fork Salmon watershed.

Change in predicted habitat capacity for Chinook salmon compared to the previous extrapolation, by life-stage, within the North Fork Salmon watershed.

Estimated chinook capacities and comparison with previous random forest extrapolations for eight watersheds
Model Watershed Predicted capacity Capacity % change Predicted capacity SE SE % change
Juv summer EF Salmon 689,267.0 34 74,826 141
Juv summer Lemhi 532,806.3 -7 23,315 33
Juv summer NF Salmon 184,759.5 -5 16,204 52
Juv summer Pahsimeroi 200,435.3 -11 8,313 -1
Juv summer Panther Cr 505,906.7 4 41,601 77
Juv summer Upper Salmon 973,874.1 37 114,743 120
Juv summer Valley Cr 467,674.0 13 72,134 117
Juv summer Yankee Fork 524,567.5 54 90,995 281
Juv winter EF Salmon 34,428.5 -75 67,228 388
Juv winter Lemhi 61,977.1 -60 28,701 325
Juv winter NF Salmon 24,708.7 -55 25,271 401
Juv winter Pahsimeroi 33,654.4 -64 15,138 123
Juv winter Panther Cr 60,186.4 -61 50,357 402
Juv winter Upper Salmon 38,599.2 -83 78,869 224
Juv winter Valley Cr 23,612.5 -82 47,311 256
Juv winter Yankee Fork 29,059.3 -71 65,686 408
Redds EF Salmon 363.3 -22 29,624 101,387
Redds Lemhi 323.3 -4 14,345 155,682
Redds NF Salmon 151.1 -14 9,143 112,226
Redds Pahsimeroi 125.6 12 6,458 169,943
Redds Panther Cr 392.8 -15 19,546 101,478
Redds Upper Salmon 517.6 -28 36,800 76,211
Redds Valley Cr 347.2 -38 22,465 64,316
Redds Yankee Fork 394.2 -44 26,929 47,844

Steelhead

Change in predicted habitat capacity for steelhead compared o the previous extrapolation, by life-stage, within the North Fork Salmon watershed..

Change in predicted habitat capacity for steelhead compared o the previous extrapolation, by life-stage, within the North Fork Salmon watershed..

Estimated winter steelhead capacities and comparison with previous random forest extrapolations for eight watersheds
Model Watershed Predicted capacity Capacity % change Predicted capacity SE SE % change
Juv summer EF Salmon 225,462.7 -40 30,958 248
Juv summer Lemhi 294,099.9 -26 19,878 190
Juv summer NF Salmon 202,904.2 -23 23,114 204
Juv summer Pahsimeroi 148,087.9 -32 9,877 61
Juv summer Panther Cr 230,228.7 -25 16,642 164
Juv summer Upper Salmon 213,209.3 -44 33,036 199
Juv summer Valley Cr 154,009.8 -45 23,262 160
Juv summer Yankee Fork 174,368.3 -46 30,533 405
Juv winter EF Salmon 180,845.7 -54 54,038 91
Juv winter Lemhi 228,750.3 -42 35,943 99
Juv winter NF Salmon 163,163.2 -48 38,960 45
Juv winter Pahsimeroi 129,045.6 -40 16,943 47
Juv winter Panther Cr 205,509.7 -35 25,593 61
Juv winter Upper Salmon 155,401.5 -63 62,129 90
Juv winter Valley Cr 130,227.9 -61 45,613 61
Juv winter Yankee Fork 150,547.5 -64 59,730 44
Redds EF Salmon 367.3 -23 31,276 113,515
Redds Lemhi 382.3 -5 22,932 139,872
Redds NF Salmon 287.0 -20 21,118 116,877
Redds Pahsimeroi 152.4 -22 12,285 137,702
Redds Panther Cr 279.7 -18 15,998 121,356
Redds Upper Salmon 393.2 -23 33,945 100,246
Redds Valley Cr 311.7 -32 23,919 86,603
Redds Yankee Fork 393.8 -34 30,994 96,783

Capacity by stream

Chinook

Steelhead